Regulatory roles of the epitranscriptome and RNA structurome during vertebrate development

项目摘要/摘要 在所有动物中，母体到受精卵的转变允许将单个受精卵所需的信息转移到 发育成成熟的生物体。受精后，母体程序由母系遗传组成 MRNAs和蛋白质，驱动细胞发育，并被合子程序取代。因为这件事 转换主要发生在转录沉默的胚胎中，它严重依赖于转录后调控。 未能适当地调控母系遗传的mRNAs通常会导致发育停滞或 异常现象。最近的研究表明，母体的mRNAs被RNA修饰， 统称为“表位转录组”，与不同的mRNA命运相关。此外，我们和其他人 在母体到受精卵的转变过程中进行了mRNA结构动态的全局分析，并确定了 在这一基本过程中，许多地区在结构上进行了重塑，其中许多地区 信使核糖核酸衰变。这些研究表明，RNA修饰和动态RNA结构正在成为 母体向受精卵转变过程中基因表达的关键调节因子。然而，详细的景观 表位转录组和动态RNA结构及其在母体到母体发育过程中的基因调控作用 合子的转变仍然鲜为人知。此外，RNA修饰和结构相互影响 调节RNA功能，但对它们如何相互作用控制基因表达知之甚少 脊椎动物的发育。我实验室的主要目标是了解表位转录组和RNA是如何 在脊椎动物的发育和发育过程中，结构分别和协同地调节基因调控网络 他们的功能障碍如何促进发育缺陷或疾病。在这里，我们假设RNA 修饰和结构与反式因子相互作用参与转录后调控 景观推动脊椎动物的发展。为了验证这一假设，我们将把斑马鱼--体内的一种 脊椎动物发育模型--及其具有创新多组学方法的遗传工具箱。超过了 未来五年，我们将检查本地转录组，以生成全球但详细的地图 在母体到受精卵的转变过程中进行表位转录，并研究特定的RNA修饰如何影响 基因表达。我们还将破译由转录组的动态区域和 分析它们对RNA调控的影响。我们将确定与RNA修饰相互作用的反式因子，并 并研究它们的功能丧失对基因表达和脊椎动物的影响 发展。最后，我们将研究RNA修饰和结构如何协同调节后 转录调控。成功完成这些调查将大大增加现有的 了解RNA修饰和结构如何协调转录后调控，并将 扩大我们对形成脊椎动物发育的分子机制的理解。

PROJECT SUMMARY/ABSTRACT In all animals, the maternal-to-zygotic transition allows the transfer of information required for a single zygote to develop into a mature organism. After fertilization, the maternal program, composed of maternally-inherited mRNAs and proteins, drives cellular development and is replaced by the zygotic program. Because this transition occurs primarily in a transcriptionally silent embryo, it relies heavily on post-transcriptional regulation. Failure to properly regulate maternally-inherited mRNAs generally leads to developmental arrest or abnormalities. Recent studies have shown that maternal mRNAs are decorated with RNA modifications, collectively known as the ‘epitranscriptome’, that correlate with different mRNA fates. Moreover, we and others performed global analyses of mRNA structure dynamics during the maternal-to-zygotic transition and identified numerous regions that are structurally remodeled during this fundamental process, many of which impact mRNA decay. These studies suggest that RNA modifications and dynamic RNA structures are emerging as key regulators of gene expression during the maternal-to-zygotic transition. However, the detailed landscape of the epitranscriptome and dynamic RNA structures, and their roles in gene regulation during the maternal-to- zygotic transition remain poorly understood. Furthermore, RNA modifications and structures affect one another to regulate RNA functions, but little is known about how they interact to control gene expression during vertebrate development. The primary goal of my lab is to understand how the epitranscriptome and RNA structures mediate gene regulatory networks, separately and cooperatively, during vertebrate development and how their dysfunction promotes developmental defects or diseases. Here, we hypothesize that RNA modifications and structures interact with trans-factors to participate in the post-transcriptional regulatory landscape driving vertebrate development. To test this hypothesis, we will combine zebrafish —an in vivo model of vertebrate development— and its genetic toolbox with innovative multi-omics approaches. Over the next five years, we will inspect the native transcriptome to generate global, yet detailed, maps of the epitranscriptome during the maternal-to-zygotic transition, and study how specific RNA modifications impact gene expression. We will also decipher the RNA folds formed by dynamic regions of the transcriptome and analyze their effect on RNA regulation. We will identify trans-factors interacting with RNA modifications and structures of interest and study the consequences of their loss-of-function on gene expression and vertebrate development. Finally, we will examine how RNA modifications and structures cooperate to modulate post- transcriptional regulation. Successful completion of these investigations will greatly increase the existing knowledge of how RNA modifications and structures orchestrate post-transcriptional regulation, and will expand our understanding of the molecular mechanisms shaping vertebrate development.